Re: [AMBER] Frequencies in AMBER, obtaining the hessian

From: David A Case <>
Date: Wed, 14 Dec 2016 08:06:20 -0500

On Wed, Dec 14, 2016, Stregone wrote:

> I would like to obtain the hessian for system, how do I do it it AMBER?
> what can I do in order to save those hessians?

You would have to modify the nmode.c or sff2.c files in
$AMBERHOME/AmberTools/src/sff; we don't have any current options to dump the
Hessian to disk. (At least that I remember: maybe someone on the list has
done this.)

> It is any form in AMBER to obtain partial hessians?

Again, you would have to modify the underlying code.

> in the 1st run of the calculation I had obtained several imaginary
> frequencies, are there any changes that I could include in order to
> make tighter the minimisations, I mean a way to reduce the number of
> imaginary frequencies ?

You should have a gradient vector with an RMS magnitude of less than 10^-8.
Going lower than this is unlikely to have any noticeable effect on the
frequencies. Depending on the size of your system, you may need to run lots
of conjugate gradient steps (thousands) before turning on Newton Raphson.
Hard to give much advice without more information, but we routinely minimize
100-residue proteins (no water) to these tolerances.


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Received on Wed Dec 14 2016 - 05:30:03 PST
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